---
title: "Ephemeroptera from Brazil"
output: 
  flexdashboard::flex_dashboard:
    
    source_code: embed
    theme: yeti
    social: menu
    css: style2.css
    
editor_options: 
  chunk_output_type: inline
---


```{r setup, include=FALSE}
knitr::opts_chunk$set(
	echo = FALSE,
	message = FALSE,
	warning = FALSE
)
library(flexdashboard)
library(tidyverse)
library(crosstalk)
library(plotly)
library(viridis)
library(gsheet)
library(leaflet.providers)
library(leaflet)
library(DT)
library(janitor)
```



```{r load data, message=FALSE, warning=FALSE, include=FALSE}
Sys.setlocale("LC_ALL", "pt_BR.UTF-8")


dat1 <- gsheet2tbl("https://docs.google.com/spreadsheets/d/1_FKOEwXyNBgc8MnzMVoQvFsl1Llae_VGNjgj5K0CaH8/edit?usp=sharing")




set.seed(1000)
dat1$lat <- round(jitter(dat1$lat, factor = 1, amount = 0.001), 4)
dat1$lon <- round(jitter(dat1$lon, factor = 1, amount = 0.001), 4)

```



```{r all table, echo=FALSE}
sd <- SharedData$new(dat1)

```


Dashboard 
============


Column {.sidebar}
-------------------------------------



### Quick filter


```{r}
filter_slider("year_record", "Restrict to years", sd, ~year_record)
filter_select("family", "Select Family", sd, ~family)
filter_select("genera", "Select Genera", sd, ~genera)
filter_select("species_name", "Select Species name", sd, ~species_name)
filter_checkbox("present_today", "Present today?", sd, ~ present_today, 
                inline = FALSE)

```


Column {.tabset}
-------------------------------------


###  Map strains

```{r}
library(RColorBrewer)
library(htmltools)
pal <- colorFactor("Set3", domain = c("Baetidae",
"Caenidae",
"Coryphoridae",
"Ephemeridae",
"Euthyplociidae",
"Leptohyphidae",
"Leptophlebiidae",
"Melanemerellidae",
"Oligoneuriidae",
"Polymitarcyidae"))

leaflet(data = sd, width = "100%") %>%
 setView(-46.8, -18.40, zoom = 4) %>%
  addProviderTiles("Esri.WorldImagery", group = "Aerial") %>%
  addProviderTiles("OpenTopoMap", group = "Terrain") %>%
  addScaleBar("bottomright") %>%
  addProviderTiles(providers$CartoDB.Voyager, group = "Default") %>%
  addLayersControl(
    baseGroups = c("Default", "Aerial", "Terrain"),
    
    options = layersControlOptions(collapsed = T)
  ) %>%
  addCircleMarkers(
  
    radius = 6,
    fillOpacity = 1,
    weight = 0.5,
    label = paste(dat1$family, "- Details"),
    fillColor = ~ pal(family),
    
    
    popup = paste(
      "
Specimen details
",
      "Family:", dat1$"family", "
",
      
      #"Genera:", dat1$"genera", "", "
",
       "Species:", dat1$"species_name", "
",
      "Author:", dat1$"author", "
",
      "Datum:", dat1$"datum", "
",
      "Geolocation:", dat1$"geolocation", "
",
        "Georeference:", dat1$"georeference", "
",
        "Geolocation:", dat1$"geolocation", "
",
        #"UC Federal", dat1$"UC_federal", "
",
        #"UC non-federal:", dat1$"UC_nofederal", "
",
        "Geolocation:", dat1$"geolocation", "
",
      #"RPPN:", dat1$"RPPN", "
",
      #"Country:", dat1$"country", "
",
      #"State:", dat1$"state", "
",
      "Municipality:", dat1$"municipality", "
",
      "Title:", dat1$"title", "
",
      "Literature source:", dat1$"author_record", "
",
      "Publication year:", dat1$"year_record", "
"
      
    )

  ) %>%
  addLegend("bottomleft",
    pal = pal,
    values = ~family,
    title = "Family",
    opacity = 1
  ) %>% 
  
  addMeasure(
    position = "bottomleft",
    primaryLengthUnit = "meters",
    primaryAreaUnit = "sqmeters",
    activeColor = "#3D535D",
    completedColor = "#7D4479") %>% 
  addEasyButton(easyButton(
    icon="fa-globe", title="Zoom to Level 4",
    onClick=JS("function(btn, map){ map.setZoom(4); }"))) 
```


###  View grid display


```{r}
dat_table <- dat1 %>% 
  select(year_record, family, genera, species_name, author, present_today, state, municipality)
                
    
    
  
datatable(dat_table,
  extensions = c("Buttons"),
  escape = FALSE, rownames = FALSE,
  class = "cell-border stripe",
    options = list(
   extensions = 'Buttons', options = list(
    dom = 'Bfrtip',
    buttons = c('copy', 'csv', 'excel', 'pdf', 'print')
  ) 
    
  )
 
)
```



###  Chart by host



```{r}


p_family <- dat1 %>% 
  tabyl(family) %>% 
  ggplot(aes(reorder(family, n), n))+
  geom_col(fill = "#558796")+
  theme_minimal()+
  coord_flip()+
  theme(legend.position = "none", 
        plot.margin = margin(2, 2, 2, 2, "cm"))+
  labs(x = "", y = "Number of records", title = "Family")
  
ggplotly(p_family)
  
  


```




About this dashboard
============



Column {.tabset}
-------------------------------------


### About this database

 Screencast video tutorial